The Northern Territory is expected to produce 3 million to 3.5 million trays of mangoes this year, down from over 4 million in 2012.
A poor wet season and warm dry season have affected flowering in Darwin's Rural Area.
The Darwin crop is expected to be down 40 per cent on last year, but Katherine is expected to fare better, producing a similar crop to 2012.
Yields might be down, but this could be a great year for growers to make money, according to president of the NT Mango Industry Association, Ross Maxwell.
"This is the year to make dollars, this is definitely the year," he said.
"With the volumes being down, the overlap (between the Darwin and Katherine harvest) is not as pronounced this year, so there'll be a nice even flow (of fruit) into the markets.
"With the lower yield and definitely not the huge volumes hitting the market at one time, it's definitely a year to look after your crop."
Mr Maxwell says the bulk of this year's NT mango crop will be picked during mid to late October and, because of a second flowering, there will be some growers picking late into November.
Super-early mangoes from the Territory have already and are getting up to $75 tray.